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Gene: VTN |
Gene summary for VTN |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | VTN | Gene ID | 7448 |
| Gene name | vitronectin | |
| Gene Alias | V75 | |
| Cytomap | 17q11.2 | |
| Gene Type | protein-coding | GO ID | GO:0001704 | UniProtAcc | D9ZGG2 |
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Malignant transformation analysis |
| Identification of the aberrant gene expression in precancerous and cancerous lesions by comparing the gene expression of stem-like cells in diseased tissues with normal stem cells |
| Malignant transformation involving gene list. |
| Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
| 7448 | VTN | NAFLD1 | Human | Liver | NAFLD | 1.58e-03 | -1.31e+00 | -0.04 |
| 7448 | VTN | S41 | Human | Liver | Cirrhotic | 7.09e-05 | -7.72e-01 | -0.0343 |
| 7448 | VTN | S42 | Human | Liver | HCC | 1.89e-02 | 1.75e-01 | -0.0103 |
| 7448 | VTN | S43 | Human | Liver | Cirrhotic | 1.77e-12 | -3.50e-02 | -0.0187 |
| 7448 | VTN | HCC1_Meng | Human | Liver | HCC | 5.26e-41 | 6.83e-01 | 0.0246 |
| 7448 | VTN | HCC2_Meng | Human | Liver | HCC | 9.41e-52 | -1.29e+00 | 0.0107 |
| 7448 | VTN | cirrhotic1 | Human | Liver | Cirrhotic | 4.18e-19 | 4.52e-01 | 0.0202 |
| 7448 | VTN | cirrhotic2 | Human | Liver | Cirrhotic | 6.28e-21 | 4.92e-01 | 0.0201 |
| 7448 | VTN | p6 | Human | Liver | Cyst | 4.18e-13 | -1.31e+00 | -0.0218 |
| 7448 | VTN | HCC1 | Human | Liver | HCC | 4.16e-25 | 5.67e+00 | 0.5336 |
| 7448 | VTN | HCC2 | Human | Liver | HCC | 5.82e-30 | 5.76e+00 | 0.5341 |
| 7448 | VTN | HCC5 | Human | Liver | HCC | 4.84e-04 | 3.37e+00 | 0.4932 |
| 7448 | VTN | Pt13.a | Human | Liver | HCC | 1.73e-24 | 9.51e-02 | 0.021 |
| 7448 | VTN | Pt13.b | Human | Liver | HCC | 3.43e-38 | 1.46e-01 | 0.0251 |
| 7448 | VTN | Pt14.a | Human | Liver | HCC | 8.89e-03 | 3.50e-01 | 0.0169 |
| 7448 | VTN | Pt14.b | Human | Liver | HCC | 2.68e-08 | 4.26e-01 | 0.018 |
| 7448 | VTN | Pt14.d | Human | Liver | HCC | 4.20e-08 | 2.87e-01 | 0.0143 |
| 7448 | VTN | S014 | Human | Liver | HCC | 9.08e-16 | 3.17e-01 | 0.2254 |
| 7448 | VTN | S015 | Human | Liver | HCC | 6.04e-09 | 1.65e-02 | 0.2375 |
| 7448 | VTN | S016 | Human | Liver | HCC | 4.54e-27 | -8.75e-01 | 0.2243 |
| Page: 1 2 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease |
| ∗log2FC in expression of this searched gene in stem-like cells from each diseased tissue sample relative to stem-like cells in normal samples in each tissue plotted against the malignancy continuum. Samples are colored based on if they are from different disease stage. |
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Malignant transformation related pathway analysis |
| Find out the enriched GO biological processes and KEGG pathways involved in transition from healthy to precancer to cancer |
| Figure of enriched GO biological processes. |
| Tissue | Disease Stage | Enriched GO biological Processes |
| Colorectum | AD |  |
| Colorectum | SER |  |
| Colorectum | MSS |  |
| Colorectum | MSI-H |  |
| Colorectum | FAP |  |
| ∗Top 15 enriched GO BP terms are showed in the bar plot of each disease state in each tissue. Each row represents a significant GO biological process which is colored according to the -log10(p.adjust). |
| Page: 1 2 3 4 5 6 7 8 9 |
| Enriched GO biological processes. |
| GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
| GO:001046621 | Liver | HCC | negative regulation of peptidase activity | 132/7958 | 262/18723 | 5.82e-03 | 2.42e-02 | 132 |
| GO:004825921 | Liver | HCC | regulation of receptor-mediated endocytosis | 60/7958 | 110/18723 | 7.12e-03 | 2.84e-02 | 60 |
| GO:004826011 | Liver | HCC | positive regulation of receptor-mediated endocytosis | 31/7958 | 52/18723 | 9.52e-03 | 3.60e-02 | 31 |
| GO:00074921 | Liver | HCC | endoderm development | 43/7958 | 77/18723 | 1.24e-02 | 4.51e-02 | 43 |
| GO:004586132 | Liver | Cyst | negative regulation of proteolysis | 25/496 | 351/18723 | 8.03e-06 | 5.72e-04 | 25 |
| GO:005254732 | Liver | Cyst | regulation of peptidase activity | 28/496 | 461/18723 | 4.37e-05 | 2.40e-03 | 28 |
| GO:004206032 | Liver | Cyst | wound healing | 26/496 | 422/18723 | 6.45e-05 | 3.28e-03 | 26 |
| GO:009030331 | Liver | Cyst | positive regulation of wound healing | 8/496 | 59/18723 | 1.55e-04 | 6.44e-03 | 8 |
| GO:005109932 | Liver | Cyst | positive regulation of binding | 14/496 | 173/18723 | 2.15e-04 | 7.99e-03 | 14 |
| GO:00075963 | Liver | Cyst | blood coagulation | 16/496 | 217/18723 | 2.29e-04 | 8.38e-03 | 16 |
| GO:005254832 | Liver | Cyst | regulation of endopeptidase activity | 25/496 | 432/18723 | 2.35e-04 | 8.42e-03 | 25 |
| GO:006104131 | Liver | Cyst | regulation of wound healing | 12/496 | 134/18723 | 2.37e-04 | 8.42e-03 | 12 |
| GO:00075993 | Liver | Cyst | hemostasis | 16/496 | 222/18723 | 2.97e-04 | 9.67e-03 | 16 |
| GO:00508173 | Liver | Cyst | coagulation | 16/496 | 222/18723 | 2.97e-04 | 9.67e-03 | 16 |
| GO:190303631 | Liver | Cyst | positive regulation of response to wounding | 8/496 | 72/18723 | 6.21e-04 | 1.76e-02 | 8 |
| GO:001046631 | Liver | Cyst | negative regulation of peptidase activity | 17/496 | 262/18723 | 6.53e-04 | 1.82e-02 | 17 |
| GO:005109832 | Liver | Cyst | regulation of binding | 21/496 | 363/18723 | 7.29e-04 | 1.98e-02 | 21 |
| GO:001095131 | Liver | Cyst | negative regulation of endopeptidase activity | 16/496 | 252/18723 | 1.17e-03 | 2.95e-02 | 16 |
| GO:190303431 | Liver | Cyst | regulation of response to wounding | 12/496 | 167/18723 | 1.68e-03 | 3.78e-02 | 12 |
| GO:00508193 | Liver | Cyst | negative regulation of coagulation | 6/496 | 53/18723 | 2.68e-03 | 4.94e-02 | 6 |
| Page: 1 2 3 4 5 6 7 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa046102 | Liver | Cirrhotic | Complement and coagulation cascades | 48/2530 | 86/8465 | 4.41e-07 | 5.44e-06 | 3.35e-06 | 48 |
| hsa0451021 | Liver | Cirrhotic | Focal adhesion | 93/2530 | 203/8465 | 9.27e-07 | 1.10e-05 | 6.80e-06 | 93 |
| hsa0520510 | Liver | Cirrhotic | Proteoglycans in cancer | 85/2530 | 205/8465 | 2.37e-04 | 1.58e-03 | 9.75e-04 | 85 |
| hsa05165 | Liver | Cirrhotic | Human papillomavirus infection | 124/2530 | 331/8465 | 1.55e-03 | 7.83e-03 | 4.83e-03 | 124 |
| hsa046103 | Liver | Cirrhotic | Complement and coagulation cascades | 48/2530 | 86/8465 | 4.41e-07 | 5.44e-06 | 3.35e-06 | 48 |
| hsa0451031 | Liver | Cirrhotic | Focal adhesion | 93/2530 | 203/8465 | 9.27e-07 | 1.10e-05 | 6.80e-06 | 93 |
| hsa0520511 | Liver | Cirrhotic | Proteoglycans in cancer | 85/2530 | 205/8465 | 2.37e-04 | 1.58e-03 | 9.75e-04 | 85 |
| hsa051651 | Liver | Cirrhotic | Human papillomavirus infection | 124/2530 | 331/8465 | 1.55e-03 | 7.83e-03 | 4.83e-03 | 124 |
| hsa0451041 | Liver | HCC | Focal adhesion | 125/4020 | 203/8465 | 3.12e-05 | 1.88e-04 | 1.04e-04 | 125 |
| hsa046104 | Liver | HCC | Complement and coagulation cascades | 57/4020 | 86/8465 | 3.19e-04 | 1.45e-03 | 8.04e-04 | 57 |
| hsa051652 | Liver | HCC | Human papillomavirus infection | 188/4020 | 331/8465 | 3.34e-04 | 1.49e-03 | 8.29e-04 | 188 |
| hsa0520521 | Liver | HCC | Proteoglycans in cancer | 121/4020 | 205/8465 | 5.22e-04 | 2.18e-03 | 1.21e-03 | 121 |
| hsa0451051 | Liver | HCC | Focal adhesion | 125/4020 | 203/8465 | 3.12e-05 | 1.88e-04 | 1.04e-04 | 125 |
| hsa046105 | Liver | HCC | Complement and coagulation cascades | 57/4020 | 86/8465 | 3.19e-04 | 1.45e-03 | 8.04e-04 | 57 |
| hsa051653 | Liver | HCC | Human papillomavirus infection | 188/4020 | 331/8465 | 3.34e-04 | 1.49e-03 | 8.29e-04 | 188 |
| hsa0520531 | Liver | HCC | Proteoglycans in cancer | 121/4020 | 205/8465 | 5.22e-04 | 2.18e-03 | 1.21e-03 | 121 |
| Page: 1 |
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Cell-cell communication analysis |
| Identification of potential cell-cell interactions between two cell types and their ligand-receptor pairs for different disease states |
| Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
| VTN | ITGA8_ITGB1 | VTN_ITGA8_ITGB1 | VTN | GC | ADJ |
| VTN | ITGAV_ITGB1 | VTN_ITGAV_ITGB1 | VTN | GC | ADJ |
| VTN | ITGA8_ITGB1 | VTN_ITGA8_ITGB1 | VTN | GC | GC |
| VTN | ITGAV_ITGB1 | VTN_ITGAV_ITGB1 | VTN | GC | GC |
| VTN | ITGAV_ITGB1 | VTN_ITGAV_ITGB1 | VTN | Liver | Healthy |
| VTN | ITGAV_ITGB5 | VTN_ITGAV_ITGB5 | VTN | Liver | Healthy |
| VTN | ITGAV_ITGB8 | VTN_ITGAV_ITGB8 | VTN | Liver | Healthy |
| VTN | ITGAV_ITGB1 | VTN_ITGAV_ITGB1 | VTN | Liver | Precancer |
| VTN | ITGAV_ITGB5 | VTN_ITGAV_ITGB5 | VTN | Liver | Precancer |
| VTN | ITGAV_ITGB8 | VTN_ITGAV_ITGB8 | VTN | Liver | Precancer |
| Page: 1 |
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Single-cell gene regulatory network inference analysis |
| Find out the significant the regulons (TFs) and the target genes of each regulon across cell types for different disease states |
| TF | Cell Type | Tissue | Disease Stage | Target Gene | RSS | Regulon Activity |
| ∗The dot plots of a searched regulon are shown for all cell subpopulations in each disease state of each tissue based on the regulon specific score inferred using pySCENIC and by calculating the average expression. |
| Page: 1 |
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Somatic mutation of malignant transformation related genes |
| Annotation of somatic variants for genes involved in malignant transformation |
| Hugo Symbol | Variant Class | Variant Classification | dbSNP RS | HGVSc | HGVSp | HGVSp Short | SWISSPROT | BIOTYPE | SIFT | PolyPhen | Tumor Sample Barcode | Tissue | Histology | Sex | Age | Stage | Therapy Types | Drugs | Outcome |
| VTN | SNV | Missense_Mutation | c.819N>G | p.Phe273Leu | p.F273L | P04004 | protein_coding | deleterious(0.04) | probably_damaging(0.949) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| VTN | SNV | Missense_Mutation | c.430N>T | p.Pro144Ser | p.P144S | P04004 | protein_coding | tolerated(0.53) | benign(0.058) | TCGA-BH-A0HF-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | |
| VTN | SNV | Missense_Mutation | novel | c.521N>A | p.Ala174Asp | p.A174D | P04004 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-BH-A18T-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
| VTN | SNV | Missense_Mutation | c.56N>A | p.Ala19Asp | p.A19D | P04004 | protein_coding | deleterious(0.03) | possibly_damaging(0.484) | TCGA-BH-A1F8-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD | |
| VTN | SNV | Missense_Mutation | rs782315239 | c.1349N>A | p.Arg450His | p.R450H | P04004 | protein_coding | deleterious(0.02) | probably_damaging(0.954) | TCGA-A6-6781-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | oxaliplatin | SD |
| VTN | SNV | Missense_Mutation | rs781937745 | c.1348N>T | p.Arg450Cys | p.R450C | P04004 | protein_coding | deleterious(0) | probably_damaging(0.954) | TCGA-AA-3496-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| VTN | SNV | Missense_Mutation | rs782315239 | c.1349N>A | p.Arg450His | p.R450H | P04004 | protein_coding | deleterious(0.02) | probably_damaging(0.954) | TCGA-AA-3510-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| VTN | SNV | Missense_Mutation | rs782244379 | c.742N>A | p.Asp248Asn | p.D248N | P04004 | protein_coding | tolerated(0.12) | benign(0.088) | TCGA-AA-3510-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| VTN | SNV | Missense_Mutation | novel | c.496N>A | p.Asp166Asn | p.D166N | P04004 | protein_coding | tolerated(0.13) | benign(0.049) | TCGA-AA-3522-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| VTN | SNV | Missense_Mutation | novel | c.746G>A | p.Gly249Asp | p.G249D | P04004 | protein_coding | tolerated(0.13) | possibly_damaging(0.565) | TCGA-AA-3947-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 |
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Related drugs of malignant transformation related genes |
| Identification of chemicals and drugs interact with genes involved in malignant transfromation |
| (DGIdb 4.0) |
| Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
| Page: 1 |
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